BioC 2.12: CHECK report for HTqPCR on petty

Package: HTqPCR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.14.0.tar.gz

StartedAt: 2013-10-08 22:46:14 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:48:45 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 151.1 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'HTqPCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTqPCR' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'HTqPCR' can be installed ... [9s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmapSig: warning in heatmap.2(data, trace = "none", density.info =
  "none", col = col, distfun = d, breaks = b, mar = mar, ...): partial
  argument match of 'mar' to 'margins'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'n' to 'number'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'sort' to 'sort.by'
plotCtCor: warning in heatmap.2(x, col = col, breaks = b, scale =
  "none", dendrogram = "row", trace = "none", main = main, density.info
  = "none", mar = mar, ...): partial argument match of 'mar' to
  'margins'
plotCtHeatmap: warning in heatmap.2(data, trace = "none", density.info
  = "none", main = main, col = col, distfun = d, breaks = breaks, mar =
  mar, ...): partial argument match of 'mar' to 'margins'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra = 0.001):
  partial argument match of 'sfra' to 'sfrac'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD.ratio[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra =
  0.001): partial argument match of 'sfra' to 'sfrac'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [43s/44s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
setCategory    10.012  0.321  10.407
HTqPCR-package  6.028  0.112   6.192
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck/00check.log'
for details.

* installing *source* package 'HTqPCR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HTqPCR)

name	user	system	elapsed
HTqPCR-package	6.028	0.112	6.192
cbind	0.266	0.002	0.281
changeCtLayout	0.213	0.003	0.222
clusterCt	0.213	0.013	0.243
filterCategory	0.263	0.004	0.267
filterCtData	0.326	0.005	0.336
heatmapSig	1.979	0.016	2.002
limmaCtData	1.112	0.010	1.151
mannwhitneyCtData	2.077	0.010	2.099
normalizeCtData	0.627	0.025	0.661
plotCVBoxes	0.268	0.005	0.276
plotCtArray	0.238	0.006	0.247
plotCtBoxes	0.091	0.004	0.096
plotCtCard	0.107	0.007	0.118
plotCtCategory	4.721	0.081	4.815
plotCtCor	0.079	0.006	0.088
plotCtDensity	0.062	0.008	0.072
plotCtHeatmap	3.574	0.065	3.979
plotCtHistogram	0.033	0.006	0.042
plotCtOverview	0.196	0.012	0.211
plotCtPCA	0.070	0.007	0.079
plotCtPairs	0.912	0.023	0.943
plotCtRQ	0.524	0.012	0.544
plotCtReps	0.194	0.008	0.214
plotCtScatter	0.044	0.007	0.059
plotCtSignificance	0.692	0.012	0.709
plotCtVariation	1.035	0.046	1.090
plotGenes	0.046	0.007	0.056
qPCRpros	0.013	0.003	0.016
qPCRraw	0.014	0.003	0.017
qPCRset-class	0.132	0.011	0.145
readCtData	0.294	0.007	0.303
setCategory	10.012	0.321	10.407
ttestCtData	1.458	0.011	1.528